BuenColors

A package that facilitates nice colors created for the Buenrostro Lab. The base of the package including some divergent color schemes were taken from the wesanderson package. This README provides a quick overview of how to use the color schemes with ggplot2 and which palettes are available.

Installation via GitHub

devtools::install_github("caleblareau/BuenColors")

Color Palettes

library(BuenColors)

With the library loaded, just type this to get either the continuous or discrete (by default) palette printed in your plot console.

jdb_palette("FantasticFox")

jdb_palette("aqua_brick", type = "continuous")

Here are all the names that are available…

#>   [1] "algae_earth"    "aqua_brick"     "aqua_tan"       "berry"         
#>   [5] "blue_cyan"      "BottleRocket"   "BottleRocket2"  "brewer_blue"   
#>   [9] "brewer_celsius" "brewer_fire"    "brewer_green"   "brewer_heat"   
#>  [13] "brewer_jamaica" "brewer_marine"  "brewer_orange"  "brewer_purple" 
#>  [17] "brewer_red"     "brewer_spectra" "brewer_violet"  "brewer_yes"    
#>  [21] "calma_azules"   "calma_bosque"   "calma_manudo"   "calma_marino"  
#>  [25] "calma_morado"   "calma_musgos"   "Cavalcanti"     "Chevalier"     
#>  [29] "china_basics"   "china_dragon"   "china_novice"   "china_ranges"  
#>  [33] "china_sunset"   "china_theory"   "china_weirdo"   "citric"        
#>  [37] "citric_yellow"  "citrus"         "cyan_brick"     "cyan_green"    
#>  [41] "cyan_pink"      "cyan_purple"    "cyan_tan"       "cyan_violet"   
#>  [45] "Darjeeling"     "Darjeeling2"    "dark_blue"      "dark_citrus"   
#>  [49] "dark_cyan"      "dark_violet"    "dusk_dawn"      "FantasticFox"  
#>  [53] "flame_artic"    "flame_blind"    "flame_flame"    "flame_light"   
#>  [57] "flame_macaw"    "flame_polar"    "flame_volts"    "flame_watts"   
#>  [61] "flame_weird"    "flame_wings"    "forest"         "forest_citric" 
#>  [65] "forest_yellow"  "GrandBudapest"  "GrandBudapest2" "horizon"       
#>  [69] "horizon_extra"  "lawhoops"       "Moonrise1"      "Moonrise2"     
#>  [73] "Moonrise3"      "ocean_aqua"     "ocean_brick"    "ocean_citrus"  
#>  [77] "ocean_earth"    "ocean_green"    "ocean_pink"     "ocean_red"     
#>  [81] "ocean_teal"     "purple_baby"    "purple_pink"    "Royal1"        
#>  [85] "Royal2"         "Rushmore"       "samba_color"    "samba_light"   
#>  [89] "samba_night"    "solar_basic"    "solar_blues"    "solar_extra"   
#>  [93] "solar_flare"    "solar_glare"    "solar_rojos"    "teal_orange"   
#>  [97] "teal_violet"    "white_grove"    "white_jungle"   "white_mango"   
#> [101] "white_orange"   "white_tango"    "wolfgang_basic" "wolfgang_extra"
#> [105] "Zissou"

Color Maps

To keep consistent color designations, one can use the color_map function to link features to their specific hex color annoations. For example,

jdb_color_map(c("HSC"))
#> [1] "#00441B"

returns the hex code associated with HSC in the Buenrostro Lab paradigm. This function may be applied over multiple features–

jdb_color_map(c("HSC", "CMP", "HSC"))
#> [1] "#00441B" "#FFC179" "#00441B"

and will error out when a feature is not recognized–

jdb_color_map(c("WHAT"))
#>  Error: all(name %in% names(jdb_color_maps)) is not TRUE

Here are all the names that are available…

#>  [1] "B"     "CD4"   "CD8"   "CLP"   "CMP"   "Ery"   "GMP"   "GMP-A"
#>  [9] "GMP-B" "GMP-C" "HSC"   "LMPP"  "MEP"   "mono"  "MPP"   "NK"   
#> [17] "pDC"

Here are what the mappings look like…

ggplot example

To coordinate a ggplot feature (e.g. data point in a scatter plot) with a particular color, this post was a life-saver. Specifically, we’ll use a named vector to coordinate the discrete values. Here’s an example–

xy <- 1:7
cell <- c("GMP-A", "Ery", "CD4", "Ery", "LMPP", "ERY", "MEP")

df <- data.frame(
  xy = xy,
  cell = cell, stringsAsFactors = FALSE
)

ggplot(df, aes(x = xy, y = xy, color = cell)) +
  geom_point(size = 10) + pretty_plot() +
  scale_color_manual(values = jdb_color_maps)
#> Warning: Removed 1 rows containing missing values (geom_point).

P.S.– this call will return a blank color for features that are not found in the color map (“ERY” in this example).

Important Note on color mappings…

The above ggplot command works because jdb_color_maps (with an ‘s’) exists as a named vector in the BuenColors NAMESPACE. The provided function (jdb_color_map) does not have an ‘s’ by the way. This same syntax of supplying a named vector should work for all discrete color scale functionalities in ggplot.

Discrete colors

The trick here is to use scale_color_manual like it is shown here–

library(ggplot2)
ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) + 
  geom_point() + pretty_plot() + 
  scale_color_manual(values = jdb_palette("brewer_spectra"))

Continuous fill

The trick here is to use scale_color_gradientn like it is shown here–

df <- data.frame(x = rnorm(1000), y = 0)
ggplot(df, aes(x=x, y=y, colour=x)) + geom_point() + 
  scale_color_gradientn(colors = jdb_palette("flame_light")) +
  pretty_plot()

Density Plot

Best way that I’ve found to make the density color function represented in the points. Thanks to Kamil Slowikowski for figuring this out.

dat <- data.frame(
  x = c(
    rnorm(1e4, mean = 0, sd = 0.1),
    rnorm(1e3, mean = 0, sd = 0.1)
  ),
  y = c(
    rnorm(1e4, mean = 0, sd = 0.1),
    rnorm(1e3, mean = 0.1, sd = 0.2)
  )
)
dat$density <- get_density(dat$x, dat$y)
ggplot2::ggplot(dat) + geom_point(aes(x, y, color = density)) + 
  scale_color_gradientn(colors = jdb_palette("solar_extra")) +
  pretty_plot()

Shuffle Plot Order

Quick wrapper using shuf to change the order of plotting points (to a random presentation) to avoid hiding effects.

tdf<-paste(system.file('rds',package='BuenColors'),'basicTSNE.rds',sep='/')
df <- readRDS(tdf)
ggplot(shuf(df)) + geom_point(aes(X1, X2, color = counts)) + 
  scale_color_gradientn(colors = jdb_palette("solar_extra")) +
  pretty_plot()

Continuous Colors

Here’s what each palette looks like on a continuous scale.

#> $algae_earth

#> 
#> $aqua_brick

#> 
#> $aqua_tan

#> 
#> $berry

#> 
#> $blue_cyan

#> 
#> $BottleRocket

#> 
#> $BottleRocket2

#> 
#> $brewer_blue

#> 
#> $brewer_celsius

#> 
#> $brewer_fire

#> 
#> $brewer_green

#> 
#> $brewer_heat

#> 
#> $brewer_jamaica

#> 
#> $brewer_marine

#> 
#> $brewer_orange

#> 
#> $brewer_purple

#> 
#> $brewer_red

#> 
#> $brewer_spectra

#> 
#> $brewer_violet

#> 
#> $brewer_yes

#> 
#> $calma_azules

#> 
#> $calma_bosque

#> 
#> $calma_manudo

#> 
#> $calma_marino

#> 
#> $calma_morado

#> 
#> $calma_musgos

#> 
#> $Cavalcanti

#> 
#> $Chevalier

#> 
#> $china_basics

#> 
#> $china_dragon

#> 
#> $china_novice

#> 
#> $china_ranges

#> 
#> $china_sunset

#> 
#> $china_theory

#> 
#> $china_weirdo

#> 
#> $citric

#> 
#> $citric_yellow

#> 
#> $citrus

#> 
#> $cyan_brick

#> 
#> $cyan_green

#> 
#> $cyan_pink

#> 
#> $cyan_purple

#> 
#> $cyan_tan

#> 
#> $cyan_violet

#> 
#> $Darjeeling

#> 
#> $Darjeeling2

#> 
#> $dark_blue

#> 
#> $dark_citrus

#> 
#> $dark_cyan

#> 
#> $dark_violet

#> 
#> $dusk_dawn

#> 
#> $FantasticFox

#> 
#> $flame_artic

#> 
#> $flame_blind

#> 
#> $flame_flame

#> 
#> $flame_light

#> 
#> $flame_macaw

#> 
#> $flame_polar

#> 
#> $flame_volts

#> 
#> $flame_watts

#> 
#> $flame_weird

#> 
#> $flame_wings

#> 
#> $forest

#> 
#> $forest_citric

#> 
#> $forest_yellow

#> 
#> $GrandBudapest

#> 
#> $GrandBudapest2

#> 
#> $horizon

#> 
#> $horizon_extra

#> 
#> $lawhoops

#> 
#> $Moonrise1

#> 
#> $Moonrise2

#> 
#> $Moonrise3

#> 
#> $ocean_aqua

#> 
#> $ocean_brick

#> 
#> $ocean_citrus

#> 
#> $ocean_earth

#> 
#> $ocean_green

#> 
#> $ocean_pink

#> 
#> $ocean_red

#> 
#> $ocean_teal

#> 
#> $purple_baby

#> 
#> $purple_pink

#> 
#> $Royal1

#> 
#> $Royal2

#> 
#> $Rushmore

#> 
#> $samba_color

#> 
#> $samba_light

#> 
#> $samba_night

#> 
#> $solar_basic

#> 
#> $solar_blues

#> 
#> $solar_extra

#> 
#> $solar_flare

#> 
#> $solar_glare

#> 
#> $solar_rojos

#> 
#> $teal_orange

#> 
#> $teal_violet

#> 
#> $white_grove

#> 
#> $white_jungle

#> 
#> $white_mango

#> 
#> $white_orange

#> 
#> $white_tango

#> 
#> $wolfgang_basic

#> 
#> $wolfgang_extra

#> 
#> $Zissou

Discrete colors

Here are the discrete color units that go into each scale. If n is small and discrete, note that the colors that are selected are read from left to right.

#> $algae_earth

#> 
#> $aqua_brick

#> 
#> $aqua_tan

#> 
#> $berry

#> 
#> $blue_cyan

#> 
#> $BottleRocket

#> 
#> $BottleRocket2

#> 
#> $brewer_blue

#> 
#> $brewer_celsius

#> 
#> $brewer_fire

#> 
#> $brewer_green

#> 
#> $brewer_heat

#> 
#> $brewer_jamaica

#> 
#> $brewer_marine

#> 
#> $brewer_orange

#> 
#> $brewer_purple

#> 
#> $brewer_red

#> 
#> $brewer_spectra

#> 
#> $brewer_violet

#> 
#> $brewer_yes

#> 
#> $calma_azules

#> 
#> $calma_bosque

#> 
#> $calma_manudo

#> 
#> $calma_marino

#> 
#> $calma_morado

#> 
#> $calma_musgos

#> 
#> $Cavalcanti

#> 
#> $Chevalier

#> 
#> $china_basics

#> 
#> $china_dragon

#> 
#> $china_novice

#> 
#> $china_ranges

#> 
#> $china_sunset

#> 
#> $china_theory

#> 
#> $china_weirdo

#> 
#> $citric

#> 
#> $citric_yellow

#> 
#> $citrus

#> 
#> $cyan_brick

#> 
#> $cyan_green

#> 
#> $cyan_pink

#> 
#> $cyan_purple

#> 
#> $cyan_tan

#> 
#> $cyan_violet

#> 
#> $Darjeeling

#> 
#> $Darjeeling2

#> 
#> $dark_blue

#> 
#> $dark_citrus

#> 
#> $dark_cyan

#> 
#> $dark_violet

#> 
#> $dusk_dawn

#> 
#> $FantasticFox

#> 
#> $flame_artic

#> 
#> $flame_blind

#> 
#> $flame_flame

#> 
#> $flame_light

#> 
#> $flame_macaw

#> 
#> $flame_polar

#> 
#> $flame_volts

#> 
#> $flame_watts

#> 
#> $flame_weird

#> 
#> $flame_wings

#> 
#> $forest

#> 
#> $forest_citric

#> 
#> $forest_yellow

#> 
#> $GrandBudapest

#> 
#> $GrandBudapest2

#> 
#> $horizon

#> 
#> $horizon_extra

#> 
#> $lawhoops

#> 
#> $Moonrise1

#> 
#> $Moonrise2

#> 
#> $Moonrise3

#> 
#> $ocean_aqua

#> 
#> $ocean_brick

#> 
#> $ocean_citrus

#> 
#> $ocean_earth

#> 
#> $ocean_green

#> 
#> $ocean_pink

#> 
#> $ocean_red

#> 
#> $ocean_teal

#> 
#> $purple_baby

#> 
#> $purple_pink

#> 
#> $Royal1

#> 
#> $Royal2

#> 
#> $Rushmore

#> 
#> $samba_color

#> 
#> $samba_light

#> 
#> $samba_night

#> 
#> $solar_basic

#> 
#> $solar_blues

#> 
#> $solar_extra

#> 
#> $solar_flare

#> 
#> $solar_glare

#> 
#> $solar_rojos

#> 
#> $teal_orange

#> 
#> $teal_violet

#> 
#> $white_grove

#> 
#> $white_jungle

#> 
#> $white_mango

#> 
#> $white_orange

#> 
#> $white_tango

#> 
#> $wolfgang_basic

#> 
#> $wolfgang_extra

#> 
#> $Zissou